Recently, a novel ammonia-oxidizing archaea (AOA)/ Thaumarchaeota strain: Nitrosotenuis cloacae SAT1（“污泥细小亚硝化菌” in Chinese）was enriched fromwastewater treatment plant, with its complete genome sequence obtrained ( Li etal,  2016,   http://www.nature.com/articles/srep23747):

 Fig1. The chromosome of Nitrosotenuis cloacae SAT1

The most interesting part of the genome analysis is the rare chromosomal invertion within the genome:

Fig2. The 3D chromosomal invertion of Nitrosotenuis cloacae SAT1, the green region indicates invertion.  

Fig.3.  Dot plot representation of the pairwise alignments of the genome of Nitrosotenuis cloacae strain SAT1 against Nitrosopumilus maritimus. In original article, this figure was Figure S5A.

  Fig.4.  Dot plot representation of the pairwise alignments of the genome of Nitrosotenuis cloacae strain SAT1 against “Ca. Nitrososphaera gargensis”.. In original article, this figure was Figure S5B.

It was noted that there was a remarkable inversion of large DNA fragment in the genome of SAT1 when comparing with Group I.1a strains , which was never found in other AOA genomes. The inverted fragment was from the site of around 0.3 Mb to 1.4 Mb, about 1.1 Mb in size, and accounted for 68% of the entire genome. It might be caused by recombination during the evolution of the strain SAT1. Similar large fragment chromosome inversions were also observed in some other bacterial strains like Staphylococcus aureus and Bacillus anthracis CDC 684, which resulted in their reduced cell growth compared with closer strains without inversion. Thus, it was likely that the relatively low growth rate of the strain SAT1 was caused by the chromosomal inversion.

Reference:

Li, Y. et al. A novel ammonia-oxidizing archaeon from wastewater treatment plant: Itsenrichment, physiological and genomic characteristics. Sci. Rep. 6, 23747; doi: 10.1038/srep23747 (2016).http://www.nature.com/articles/srep23747

genome sequence: Genbank accession number: CP011097.2: http://www.ncbi.nlm.nih.gov/nuccore/CP011097.2
genome sequence: KEGG database: http://www.genome.jp/dbget-bin/www_bget?genome:T03883